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Latest improvements for QIAGEN CLC Main Workbench

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QIAGEN CLC Main Workbench 21.0.4

Release date: 2021-05-20

Bug fixes

  • Fixed an issue that caused Download Blast Databases to occasionally fail when downloading a subset of databases from NCBI.
  • Fixed an issue where deleting a portion of a sequence could cause an error to be reported.
  • Fixed an issue where an error was produced when working with outputs of Design Primers when options in the side panel under Primer info were selected. The error appeared when the mouse cursor was subsequently moved over the sequence.
  • Fixed an issue where an error resulted when trying to do the following actions when working with sequences in sequence lists: Insert Restriction Site Before/After Selection, Digest All and Create Restriction Map, Show Enzymes Cutting Inside/Outside Selection.
  • Fixed an issue that caused an occasional error to arise when deleting bases in a circular sequence that also have restriction sites.
  • Fixed an issue affecting Cloning Editor where switching between linear and circular sequence representations could cause the editor to report an error.
  • Fixed an issue where Cloning Editor occasionally reported an error when running in Viewing Mode.
  • Fixed issues present when working with Sanger assemblies when the “Lock top sequence” viewing option was enabled. Issues included not being able to scale the trace data, problems selecting bases in the sequences, and the right-click menu not offering the expected options.
  • Fixed an issue where dragging the edge of contigs in Sanger assemblies beyond the viewing area caused the horizontal scroll bar to keep scrolling.
  • Fixed an issue affecting Batch Rename, where if the term to be replaced in element names was not present, the names were deleted.
  • Fixed an issue affecting naming patterns in export tools, and in workflow output and export elements, where upper case text within curly brackets in these patterns was translated to lower case when naming the outputs.
  • Fixed an issue affecting workflows containing Iterate elements connected to more than one downstream element, where the batch overview step in the launch wizard to displayed the same input objects multiple times. This was a problem in presentation only. It did not affect the analyses.
  • Fixed an issue affecting workflows containing Iterate elements when the names of input data element contained characters considered special by the operating system (e.g. on Windows : < > | ). When affected by this issue, no outputs would be produced or just a Workflow Result Metadata table would be produced.
  • Fixed an issue affecting the Table view of long Sequence Lists, where the contents of the ‘Linear’ column could be missing for some sequences.
  • Fixed an issue where table export of a Venn diagram did not export all the columns selected in the wizard.
  • Fixed an issue affecting metadata tables where the paths to data elements that had been moved were not updated to reflect the new location.
  • Various minor bugfixes

Plugin notes

Changes have been made that improve the speed of jobs on the CLC Genomics Cloud Engine (GCE) that involve large CLC data elements. This improvement affects systems where the Cloud Plugin is installed and Cloud Connection settings have been configured.



QIAGEN CLC Main Workbench 21.0.3

Release date: 2021-01-26

There are no changes to QIAGEN CLC Main Workbench 21.0.3 relative to version 21.0.2. Version 21.0.3 has been released as the corresponding client version for QIAGEN CLC Genomics Server 21.0.3.



QIAGEN CLC Main Workbench 21.0.2

Release date: 2021-01-21

Improvements and bug fixes

  • Fixed an issue that prevented the use of saved view settings that included additional restriction enzymes (configured via the side panel settings). This issue could cause an error message to arise when the saved view settings were applied directly to an open sequence or sequence list, or when such view settings were applied generally for sequences in the Workbench Preferences.
  • Fixed an issue where changes to the list of motifs, made via the side panel settings of sequences, were not saved when that view setting was saved.
  • Fixed an issue where where the axis on a log plot could show the wrong value when zoomed out to the point where there were multiple orders of magnitudes between the indicators.
  • Various minor improvements


QIAGEN CLC Main Workbench 21.0.1

Release date: 2021-01-12

Bug fixes

  • Fixed an issue introduced in CLC Main Workbench 21.0, where stand-alone read mappings could not be opened.
  • The Java version bundled with CLC Main Workbench 21.0.1 is Java 11.0.6, where we use the JRE from AdoptOpenJDK. This addresses an issue present in Java 11.0.8, included with CLC Main Workbench 21.0, which could cause Java applications on mac systems to crash when switching keyboard layouts.

Please see the release notes for CLC Main Workbench 21.0, below, for a full list of changes since the last general release of this software.



QIAGEN CLC Main Workbench 21.0

Release date: 2021-01-12

New features and improvements

Full workflow support for Sanger sequence analysis

New features have been introduced, and improvements made, to support automated analyses of Sanger trace data using workflows.

Trim Sequences
  • Trim Sequences can now be used in workflows.
  • Trim Sequences can be run on the CLC Genomics Server.
  • A new sequence element containing the trimmed sequences is output. Previously, the input was modified and saved.
  • A report can be generated containing a summary of the number of reads trimmed and the reasons for the trimming.
  • The UniVec database used in this tool has been updated to version 10.0 of UniVec_Core.
Extract Consensus Sequence
Other improvements supporting trace data analysis in workflows
  • Trace data can be imported using on-the-fly import in workflows.
  • Improved output naming by the Assemble Sequences to Reference and Assemble Sequences tools: The sample name is included in the file name and the sequence names in the output.
  • Metadata-based naming is supported in workflows run in batch mode or with Iterate control flow elements through the use of new placeholders: {metadata} and {metadata:<columnname>}.
  • The Secondary Peak Calling tool no longer modifies the input data element, but instead produces new elements as output. Note: This change requires that the workflows with this tool that were created in older versions of the software must be manually updated. The old workflow element must be replaced by a new one. The recommended upgrade path for installed workflows containing the Secondary Peak Calling tool is to save a copy of the workflow in the Navigation Area using a version CLC Main Workbench 20.x, and then open and manually update that workflow in CLC Main Workbench 21.0. The new workflow can then be installed, if desired.
Combine Reports

The Combine Reports tool summarizes information from multiple reports and produces a single report. Previously this tool was only available in the CLC Genomics Workbench.

Workflow related
  • When a workflow with Export elements is run in batch mode, the exported files from each batch run can be saved to separate folders.
  • On-the-fly import can be used without metadata when running workflows in batch mode, and when running workflows containing a single Iterate element.
  • Name placeholders for output elements and export elements have been updated, and the naming of outputs of workflows run in batch mode can be more finely controlled.
  • Improvements for Workflow Input elements:
    • Workflow Input elements can be configured to limit the data input method to either selection of data elements from the Navigation Area or selection of files to be imported using on-the-fly import. The default is to allow the input method to be chosen when launching the workflow.
    • Workflow Input elements can be configured to limit the on-the-fly import types available when launching the workflow. Parameters of selected importers can also be locked or unlocked, as desired, defining whether the setting is configurable when launching the workflow.
  • Additional configuration options for Iterate and Collect and Distribute workflow elements are available.
  • When a workflow with Iterate elements is run with the “Batch” checkbox checked, the “Batch identifier” column in the Workflow Result Metadata table will contain the combined batch identifier, reflecting all levels of batching and iterations.
Performance improvements
  • Improved the performance of the alignment editor for large alignments.
  • Create Tree is significantly faster when creating large trees when using the Jukes-Cantor distance measure.
  • Fixed an issue that could cause the CLC Workbench to become unresponsive when exporting large binding site tables generated by Find Binding Sites and Create Fragments.
  • Improved the performance of searching for data elements associated with a metadata table when using the “Find Associated Data” button.
  • Fixed an error that occurred when displaying very large trees.
  • Performance has been improved when tools generating a large number of sequences (for example, Trim Reads) are run on a system with many threads.
Working with tables
  • Column order can be adjusted when viewing tables, and the revised column order will be respected when exporting the open table to, for example, csv or excel format files.
  • Tables in reports can be opened in a new tab: right click -> Open Table.
  • Tables can be exported using a right-click option: “File” -> “Export Table”. The export takes into account filtering, ordering and deselection of columns.
Export
  • Exported files can be saved into subfolders of the selected output area by using a forward slash character / at the start of the custom file name definition.
  • Graphics export of Sequences, Alignments and Read mappings is supported as a standard export, which can be embedded into workflows and executed on a CLC Genomics Server. This feature is intended for high-throughput applications. For other applications, we recommend the existing graphic export tool.
Create Protein Report

Updates have been made relating to the BLAST functionality in Create Protein Report:

  • The default expect value (e-value) for BLAST searches at the NCBI is 0.05, aligning with the defaults used at the NCBI.
  • The top 10 BLAST alignments are included in the report, where previously it was the top 100. The full BLAST report continues to be available by clicking on the results in the report, and the full BLAST hit table continues to be included in the report.
  • Results of searches against local sequences or databases can no longer be included in the report. (The standard BLAST tool remains available for running local searches.)
Improvements relating to connections to a CLC Server
  • The CLC Server connection dialog will present information like the version and port of the selected CLC Server prior to login, when that information is available.
  • The CLC Server connection dialog will close automatically after the “Log In” button is clicked. The login process runs in the background, indicated by a flashing server icon in the lower left corner of the Workbench.
  • When the Workbench loses connection to a CLC Server, it attempts to reestablish the connection. Open views of data stored on the CLC Server are not closed.
  • When selecting files stored on a CLC Server, only files with the relevant extensions are listed, together with their date of last modification and the size of the files.
Other improvements
  • Stand-alone Read Mapping, Contig and BLAST Graphics views support wrapped sequence layouts. The relevant option is available in the side panel. This may be of particular interest when working with Sanger trace data.
  • Import Metadata uses the name of the imported spreadsheet when naming the resulting metadata table.
  • The element History view has been updated, and its performance has been improved when handling many history entries.
  • Improved the rendering of annotations in the Export Graphics tool when used with the “Export whole area” option.
  • When hovering the mouse cursor over a Sequence List in the Navigation Area, the tooltip includes information about the sequencing platform, if this information is available.
  • The log can be saved as part of the output when running a tool or workflow in the Workbench.
  • Data locations can be added when using the Workbench in Viewing Mode.
  • Custom attributes can be configured in a data location such that attribute values are not copied when copying data elements.

Bug fixes

  • Fixed an issue affecting annotations of restriction sites for enzymes cutting within the recognition site, where the arms indicating the cut site spanned large sequence regions, instead of indicating the cut site.
  • Fixed an issue where the Search for Sequences at NCBI tool would occasionally return fewer rows than configured in the ‘Number of hits’ preference setting.
  • Fixed an issue where “Reset tree topology” in the phylogenetic tree editor could fail in some cases when input sequences were extracted from (at least) two different trees.
  • Fixed an issue where external files could not be opened on Windows Server 2019.
  • Fixed an issue where the Ctrl+F keyboard shortcut did not activate the ‘Find’ side panel when viewing a track list.
  • – Fixed an issue where, on Mac OS, clicking CLC URLs (“clc://…”) would open an older version of the Workbench even after installing a new version.
    – The list of file types automatically associated with the Workbench has been updated to only include CLC files (xxx.clc). On Mac OS only, the Workbenches would previously be associated with the set of file types that can be imported using the ‘Standard Import’ tool. The Workbench can still be associated to any given file type using the standard tools of the operating system in question.
  • Fixed an issue where a path specified in the path.properties configuration file was not properly interpreted if it was specified in ‘Windows syntax’, e.g. “x:\myDrive\temp”
  • Fixed an issue in Excel importer, where the presence of certain formulas would previously prevent successful import.
  • Fixed an issue where, if BLAST at NCBI failed with an error, no error would be shown and instead no hits were returned.
  • Fixed an issue where some workflows using a Collect and Distribute element with multiple output channels did not pass the correct inputs to a tool after the Collect and Distribute element.
  • Fixed an issue where compressed data elements sometimes appeared to have “Compression enabled: No” in the Element Info tab.
  • Fixed an issue in the Navigation Area that caused move operations to be converted to copy operations if the Navigation Area was refreshed before the move was completed.
  • Various minor bug fixes

Changes

  • The Java version bundled with CLC Main Workbench 21.0 is Java 11.08, where we use the JRE from AdoptOpenJDK.
  • The default base name for the element being exported is designated using the placeholder {name}, instead of {input}. The numeric equivalent, {1}, is unchanged. The default export naming pattern has correspondingly been changed to {name}.{extension}. (GxS notes only, add the following: This change also applies to exports configured in External Applications.) Previously {input} was used.
  • The default expect value (e-value) for BLAST at NCBI is 0.05 and the maximum number of hits is 5000, aligning with the defaults used at the NCBI.
  • Changes have been made to the handling of sequence identifiers when using Create BLAST Database. This change allows continued flexibility in the naming of sequences used for making these databases, avoiding direct exposure to limitations present in the underlying BLAST+ program, makeblastdb, such as not allowing long or duplicate sequence names. Further details are provided in our FAQ area.

Functionality retirement

Tools

  • Reverse Sequence